Drexel University Chemistry Department
PISB Organic Instrumentation Lab
Perkin-Elmer Spectrum Two FTIR
Brief Operating Instructions
Important Notes:
This instrument may be turned off when not in use.
Allow at least 10 minutes for the source to warm up before use.
Sign the instrument log book before using the instrument.
The Perkin-Elmer (PE) Spectrum Two Fourier-Transform Infrared (FTIR) Absorption
instrument is capable of using two different sampling accessories: a standard transmission
accessory and the uATR Two Universal Attenuated Total Reflectance Accessory. The
transmission accessory may be used for liquid samples analyzed neat using salt plates or solids
using a mull or KBr pellet technique. The uATR can be used for both solid and liquid samples
with little to no preparation and really should be the method of choice. Carefully install the
appropriate sampling accessory in the instrument. Note that the sampling accessory can be
changed while the instrument is turned on. The software will automatically recognize which
accessory is installed and set the software defaults appropriately.
To prepare the uATR for use:
1) Loosen the green sample hold-down arm (“lefty-loosey, righty-tighty”), swing it towards
the back of the instrument and remove the white plastic cover-plate.
2) Clean the surface of the diamond (the square crystal in the middle of the plate) using a
Kimwipe wet with an appropriate solvent. DO NOT spray any liquid directly onto the
diamond or the surrounding stainless steel sample plate surface. Organic solvents can
damage the plastic case of the instrument!
3) You must take a background spectrum using the Spectrum software (see instructions
below) before placing a sample on the uATR.
To analyze liquid samples on the uATR:
1) Place a small drop of the liquid on the surface of the diamond.
2) Place a glass microscope slide on top of the liquid to slow down the evaporation of the
sample. DO NOT press the liquid to the diamond surface to measure the spectrum.
3) Collect a spectrum of the sample as described below.
4) To clean the uATR after use with a liquid sample:
a. Wipe off the excess liquid sample using a dry Kimwipe.
b. Clean the surface of the sample plate (including the diamond) using a Kimwipe
wet with an appropriate solvent. DO NOT spray any liquid directly onto the
diamond or the surrounding stainless steel sample plate surface.
To analyze solid samples on the uATR:
1) Cover the surface of the diamond with a thin layer of the solid sample powder. Note that
solids composed of larger, hard crystals may first need to be ground into a powder using
an agate mortar and pestle to obtain a high quality IR spectrum.
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PE Spectrum 2 FTIR Operating Instructions
2) Place a glass microscope slide on top of the solid. Swing the green sample hold-down
arm forward. To obtain a good spectrum you will need to press the solid against the
surface of the diamond by tightening the green sample hold-down arm. There is a force
gauge in the Spectrum software that should be used as a guide- you should apply a force
of approximately 90 units.
3) Collect a spectrum of the sample as described below.
4) To clean the uATR after use with a solid sample:
a. Loosen the green sample hold-down arm and swing it back out of the way.
b. Remove the glass microscope slide; in most cases the solid will stick to the slide.
c. Clean the surface of the sample plate (including the diamond) and the glass
microscope slide using a Kimwipe wet with an appropriate solvent. DO NOT
spray any liquid directly onto the diamond or the surrounding stainless steel
sample plate surface.
When the instrument is not in use, replace the white plastic cover-plate on the uATR and lightly
tighten the green sample hold-down arm to hold it in place.
To analyze liquid samples using the transmission accessory you will use 1” diameter NaCl plates
located in the dessicator next to the instrument.
To analyze liquid samples (neat) on the transmission accessory:
1. Place a small drop of the liquid on the top surface of a salt plate.
2. Place a second salt plate on top of the drop of liquid. The liquid should spread out
completely between the plates, which should now be held together by the capillary action
of the liquid.
3. Place the sandwiched salt plates into the holder in the transmission accessory.
4. Collect a spectrum of the sample as described below.
5. To clean the salt plates after use with a liquid sample:
a. Wipe off the excess liquid sample using a dry Kimwipe.
b. Clean the surface of the salt plate using a Kimwipe wet with an appropriate
solvent.
To analyze solid samples on the transmission accessory (preparing a “mull”):
1. Grind a small quantity of the solid sample into a fine powder using the agate mortar &
pestle. The finer the particles, the less scattering will be observed in the IR spectrum.
2. Mix the powder with a drop or two of the chosen mulling liquid (either Nujol (mineral)
oil or fluorolube) in the mortar. This should produce a loose paste called a mull.
3. Place a small drop of the mull on the surface of a salt plate.
4. Place a second salt plate on top of the mull. It should spread out completely between the
plates, which should now be held together by the capillary action of the liquid.
5. Place the sandwiched salt plates into the holder in the transmission accessory.
6. Collect a spectrum of the sample as described below.
7. To clean the salt plates after use with a mull sample:
a. Wipe off the excess sample/oil using a dry Kimwipe.
b. Clean the surface of the salt plate using a Kimwipe wet with an appropriate
solvent.
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PE Spectrum 2 FTIR Operating Instructions
Collecting an infrared spectrum using the PE Spectrum v10.03.02 software:
1) Start the Spectrum software by double clicking the icon on the Desktop. Enter the
appropriate Username and Password, then press OK to continue. You will now be in the
main program window.
2) You should check the spectrum collection settings on the Setup Instrument Basic tab at
the bottom of the main window. Typical settings for the ATR are: Start: 4000 cm-1, End:
450 cm-1, Resolution 4 cm-1, Scan type: Sample and Accumulations: 4 scans.
3) Collect a background spectrum by pressing the Background button on the icon bar
located at the top of the window. The view in the window will change; a progress bar will
show the progress of the background collection. You should collect a background
spectrum when you first start the program, then anytime you feel the background may
have changed.
4) Enter a desired filename in the Sample ID box located at the left in the top icon bar (or
accept the default filename). The default filename can be set by selecting the Setup
Instrument Auto-Name tab. Enter a text description of the sample in the Description box
also located in the top icon bar (this text will be stored directly in the file with the data!)
5) Place a sample on the uATR following the instructions above.
6) Press the Scan button on the top icon bar to see a preview of your data (make sure the
preview button next to the scan button is selected). This is particularly important for solid
samples, as you will now see the force gauge. Tighten the green sample hold-down arm
until a force of approximately 90 is applied; you should see a good quality IR spectrum
appear.
7) Note that you are only viewing a preview of the spectrum; press the Scan button again to
collect the data and save it to the data file name you entered. When data collection is
finished you will return to the main program window automatically.
8) IMPORTANT: All data collected on the uATR sampling accessory should be processed
with the ATR correction. To do so, select the Process menu, then ATR correction. A new
window will appear showing the correction results (the default parameter of 0 should
work ok). Press OK to finish. Note that you must save the corrected spectrum separately.
With the spectrum to be saved highlighted, select the File menu, then Save (or Save As to
change the filename).
9) To automatically search the libraries installed in the software to attempt to identify the
compound, collect the data by pressing the Scanalyze rather than the Scan button. If a
spectrum is already collected, you can search it against the libraries by selecting the
Process menu, then Search, and Search for Spectra.
10) Note the tabs immediately above the spectrum. Select Samples View 1 to see the full
spectrum view.
Important Operational Notes:
If you suspect the surface of the diamond might be contaminated (because you see extraneous
peaks in a spectrum), you should clean the surface with a series of solvents spanning the entire
polarity range (such as methanol, acetone, THF and hexane). Remember to always wet a
Kimwipe with the appropriate solvent- DO NOT spray any liquid directly onto the diamond or
the surrounding stainless steel sample plate surface.
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PE Spectrum 2 FTIR Operating Instructions
For the transmission accessory, take the background spectrum with the beam path empty, i.e., do
not place two dry salt plates in the beam path. For the uATR accessory, take the background
spectrum with nothing in contact with the diamond, i.e., do not place a glass slide on top of the
diamond.
The Spectrum program is very complicated. Full details for running it are located in the PDF
manuals available in the PE Spectrum Two Manuals folder located on the computer Desktop.
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